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  <div class="section" id="lammps">
<h1>lammps<a class="headerlink" href="#lammps" title="Permalink to this headline">¶</a></h1>
<div class="section" id="classes">
<h2>Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="atomman.lammps.Log.html">Log</a></li>
<li class="toctree-l1"><a class="reference internal" href="atomman.lammps.NEBLog.html">NEBLog</a></li>
<li class="toctree-l1"><a class="reference internal" href="atomman.lammps.LammpsError.html">LammpsError</a></li>
</ul>
</div>
</div>
<div class="section" id="module-atomman.lammps">
<span id="functions-and-attributes"></span><h2>Functions and attributes<a class="headerlink" href="#module-atomman.lammps" title="Permalink to this headline">¶</a></h2>
<dl class="function">
<dt id="atomman.lammps.checkversion">
<code class="sig-prename descclassname">atomman.lammps.</code><code class="sig-name descname">checkversion</code><span class="sig-paren">(</span><em class="sig-param">lammps_command</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.lammps.checkversion" title="Permalink to this definition">¶</a></dt>
<dd><p>Gets the LAMMPS version and date information by testing lammps_command.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>lammps_command</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a>) – A LAMMPS executable.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><strong>version_info</strong> – Dictionary containing ‘version’, the str LAMMPS version, and
‘date’, the corresponding  datetime.date for the LAMMPS
version.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.9)">dict</a></p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.9)"><strong>ValueError</strong></a> – If lammps fails to run</p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.lammps.run">
<code class="sig-prename descclassname">atomman.lammps.</code><code class="sig-name descname">run</code><span class="sig-paren">(</span><em class="sig-param">lammps_command</em>, <em class="sig-param">script_name=None</em>, <em class="sig-param">script=None</em>, <em class="sig-param">mpi_command=None</em>, <em class="sig-param">restart_script_name=None</em>, <em class="sig-param">restart_script=None</em>, <em class="sig-param">logfile='log.lammps'</em>, <em class="sig-param">screen=True</em>, <em class="sig-param">suffix=None</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.lammps.run" title="Permalink to this definition">¶</a></dt>
<dd><p>Calls LAMMPS to run. Returns a Log object of the screen/logfile output.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>lammps_command</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a>) – The LAMMPS inline run command (sans -in script_name).</p></li>
<li><p><strong>script_name</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – Path of the LAMMPS input script file to use.  Either script_name or
script must be given.</p></li>
<li><p><strong>script</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – The LAMMPS input script command lines to use.  Either script_name or
script must be given.</p></li>
<li><p><strong>mpi_command</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – The MPI inline command to run LAMMPS in parallel. Default value is
None (no mpi).</p></li>
<li><p><strong>restart_script_name</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – Path to an alternate LAMMPS input script file to use for restart runs.
If given, the restart script will be used if the specified logfile
already exists.  Requires logfile to not be None.</p></li>
<li><p><strong>restart_script</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – Alternate LAMMPS script command lines to use for restart runs.
If given, the restart script will be used if the specified logfile
already exists.  Requires logfile to not be None.</p></li>
<li><p><strong>logfile</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.9)"><em>None</em></a><em>, </em><em>optional</em>) – Specifies the path to the logfile to write to.  Default value is
‘log.lammps’.  If set to None, then no logfile will be created.</p></li>
<li><p><strong>screen</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – If True (default), then the resulting Log object is built from the
LAMMPS screen output.  If False, then LAMMPS outputs no screen info
and the Log object will be built by reading logfile.</p></li>
<li><p><strong>suffix</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – Allows for the LAMMPS suffix option to be specified to use any of the
accelerated versions of pair styles if available.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Contains the processed screen/logfile contents.  Will not be returned
if logfile is None and screen is False as there would be no means to
capture the LAMMPS output.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference internal" href="atomman.lammps.Log.html#atomman.lammps.Log" title="atomman.lammps.Log">atomman.lammps.Log</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.lammps.normalize">
<code class="sig-prename descclassname">atomman.lammps.</code><code class="sig-name descname">normalize</code><span class="sig-paren">(</span><em class="sig-param">system</em>, <em class="sig-param">return_transform=False</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.lammps.normalize" title="Permalink to this definition">¶</a></dt>
<dd><p>The normalize function takes any arbitrary system and transforms it to
be compatible with LAMMPS.  In particular, LAMMPS systems must have:
1. Right-handed box vectors.
2. avect = [lx, 0.0, 0.0]
3. bvect = [xy, ly,  0.0]
4. cvect = [xz, yz,  lz]
5. All atoms initially inside the box dimensions.
Note: large box tilt factors are not adjusted with this function.
As such, the LAMMPS command ‘box tilt large’ may be needed.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>system</strong> (<a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System"><em>atomman.System</em></a>) – The system to normalize.</p></li>
<li><p><strong>return_transform</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – Indicates if the transformation matrix used during the normalization
is to be returned as well.  Default value is False</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><ul class="simple">
<li><p><strong>newsystem</strong> (<em>atomman.System</em>) – A new system that has been normalized.</p></li>
<li><p><strong>transform</strong> (<em>np.ndarray</em>) – The transformation matrix associated with the normalization.  Returned
if return_transform is True.</p></li>
</ul>
</p>
</dd>
</dl>
</dd></dl>

<span class="target" id="module-atomman.lammps.style"></span><span class="target" id="module-atomman.lammps.Potential"></span><dl class="field-list simple">
<dt class="field-odd">members</dt>
<dd class="field-odd"><p></p></dd>
<dt class="field-even">undoc-members</dt>
<dd class="field-even"><p></p></dd>
<dt class="field-odd">show-inheritance</dt>
<dd class="field-odd"><p></p></dd>
</dl>
<dl class="function">
<dt id="atomman.lammps.style.timestep">
<code class="sig-prename descclassname">atomman.lammps.style.</code><code class="sig-name descname">timestep</code><span class="sig-paren">(</span><em class="sig-param">units='metal'</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.lammps.style.timestep" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the default timestep value for a LAMMPS unit style option.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>units</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – The LAMMPS unit option.  Default value is ‘metal’</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The default timestep value.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)">float</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.lammps.style.unit">
<code class="sig-prename descclassname">atomman.lammps.style.</code><code class="sig-name descname">unit</code><span class="sig-paren">(</span><em class="sig-param">units='metal'</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.lammps.style.unit" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the units information associated with a LAMMPS units option.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>units</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – The LAMMPS unit option.  Default value is ‘metal’</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The keys are physical quantity types and the values are the associated
units to use.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.9)">dict</a></p>
</dd>
</dl>
</dd></dl>

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  <h3><a href="index.html">Table of Contents</a></h3>
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<li><a class="reference internal" href="#">lammps</a><ul>
<li><a class="reference internal" href="#classes">Classes</a></li>
<li><a class="reference internal" href="#module-atomman.lammps">Functions and attributes</a></li>
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